Just as they do every Thursday morning, nearly a dozen members from the Oasis Women’s group for homeless and recently housed women met for fellowship inside a Beacon Hill church.

But this Thursday was different. About 10:30 a.m., federal agents armed with search warrants swooped into the Swedenborgian Church on the Hill. “They started saying, ‘Nobody move. Nobody leave,’ ” said Brenda Poliskey, who has attended the meetings for a year. “I had to take a Valium to calm down.”

The investigators, from the FBI and IRS, disrupted the women’s bingo game, Poliskey said. Investigators wrote down the names of all the women in the group and ­ordered them out. Church staff members were told to stay put, she said.

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Allison Mahan, a spokeswoman for the FBI, said Thursday morning that federal investigators were executing a search warrant at the Bowdoin Street church and at an adjacent apartment building owned by the church.

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Mahan and IRS spokeswoman Jessica Crocker said the investigation was not related to the Boston Marathon bombings.

“There was a search today at the church and its apartment building directed at one employee,” said Nick Carter, a lawyer for the church. “It was not directed at the church.”

Carter, who declined to name the employee, said the church is cooperating with the investigation.

Investigators remained at the Swedenborgian Church on the Hill through the afternoon. On Thursday afternoon, people were not allowed into the church, which sits across from the State House.

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Residents, however, could enter the 18-story Bostonview Apartment building. For a time, however, they were barred from the 18th floor, where the apartment office was located.

Jesus Rodriguez showed up Thursday afternoon to help church staff set up for a rooftop party held annually at the apartment complex. Agents wouldn’t let him in the church. So, he stood outside, calling church staff in vain.

“I never heard of this,” Rodriguez said. “It’s very weird. I have never seen this go on before.”

Rodriguez credits the church with helping get his life back on track. He was homeless when he began attending more than four years ago.

By 4:25 p.m. Thursday, investigators began lugging evidence from the church and loading it into a van. Red evidence tape sealed brown paper bags and cardboard boxes, some marked “old vendor files” and “Bostonview Board.”

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The church has been embroiled in controversy in the past, with allegations that Edward J. MacKenzie Jr., a self-proclaimed henchman for mobster James “Whitey” Bulger, and other church leaders tried to loot one of the city’s more obscure congregations. A federal judge threw out a 2004 lawsuit filed against church leadership.

The Boston Society of the New Jerusalem runs the Swedenborgian Church on Bowdoin Street. The small Protestant sect follows the teachings of the 18th-century Swedish scientist and philosopher Emanuel Swedenborg.

According to the church’s website, MacKenzie is the director of operations and sits on Bostonview’s board of directors. Attempts to reach MacKenzie on Thursday were unsuccessful.

John R. Ellement and Michael Rezendes of the Globe staff contributed to this report. Akilah Johnson can be reached at ajohnson@globe.com. Follow her on Twitter @akjohnson1922.